Data post-processing questions about lammps+plumed

lue611 · January 22, 2024, 4:13am

Hi
I am using plumed+lammps to do on the fly probability enhanced sampling with two cv’s, how can I get the 2D free energy surface (FES) as below. the script FES_from_Reweighting.py seems to only get 1D?

here is the related link:
https://www.plumed.org/doc-v2.9/user-doc/html/masterclass-22-03.html
and the script is downloaded here:

github.com

invemichele/masterclass-22-03/blob/0fed1472f830e6e98377a17975aca066220ed492/scripts/FES_from_Reweighting.py

#! /usr/bin/env python3

### Get the FES estimate from reweighting. 1D or 2D only ###
# uses a weighted kernel density estimation, so it requires the bandwidth sigma
# usage is similar to plumed sum_hills

# NB: in case of multiple walkers one should combine them in a single file
# when using --stride or --skiprows one should sort them:
#   sort -gs COLVAR.* > COLVAR
# when using --blocks it is better to concatenate them:
#   cat COLVAR.* > COLVAR

import sys
import argparse
import numpy as np
import pandas as pd #much faster reading from file
do_bck=False #backup files in plumed style
if do_bck:
  bck_script='bck.meup.sh' #e.g. place the script in your ~/bin
  import subprocess

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akohlmey · January 22, 2024, 8:14am

This is a question better suited for the Plumed users forum, https://groups.google.com/g/plumed-users, since it has next to nothing to do with LAMMPS.